There's list here: https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software or this might help:

https://www.researchgate.net/post/Does_anyone_know_any_software_to_predict_3D_structure_of_ssDNA_aptamer_30mer_oligonucleotide

Please view the attached pdf..

Hi, Ahmed.

I am not an expert in this area but, looking at the internet, I expect I have found a few tools that maybe will help you.

https://haddock.science.uu.nl/dna/dna.php

http://2016.igem.org/Team:INSA-Lyon/Software (seems exactly what you want)

https://academic.oup.com/bioinformatics/article/32/2/161/1743600 (In a bioinformatics book)

http://aptani.unimore.it/

There are some papers that may help you too

Article Computational Methods for Modeling Aptamers and Designing Riboswitches

Article Using RNA Sequence and Structure for the Prediction of Ribos...

And another forum talking about something alike

https://www.biostars.org/p/125636/

Hoping to help you a bit.

All the best.

Dear All,

Thanks for your valuable comments.

I just saw this paper Article Do It Yourself 3-Dimensional Aptamer-Ligand Molecular Modeling

it might be helpful